I agree with vsmith about The General - was one of my all-time favourite films as a kid (friends thought I was really odd but that's another story!).
Titfield Thunderbolt is also a great film and well worth hunting down - you can model the trains involved in that pretty easily, though "Thunderbolt" itself is a rather tricky project.
Others on my list: The Railroader - might actually be "The Railrodder" - the writing on our video cassette is a little unclear! (another Buster Keaton, this time crossing Canada on a maintainance trolley/speeder). Von Ryan's Express is also good, though if you like your war films a little grittier The Train might be more to your tastes. Silver Streak is also good - think it may well have led me to want a full set of stainless-steel streamliners!
Ones I really can't stand - Atomic Train (so bad it's funny) and Mission Impossible - ok, I can accept the plot events, but why did they not use the proper train in the Channel Tunnel sequence? Would have been just as easy to build a Eurostar mockup instead of the TGV one.
One that really shouldn't have got past editing: The most recent version of "Murder on the Orient Express" - apart from the terrible acting, over-young Poirot, and anachronistic modern-day setting, there's one sequence where a crossing bell can clearly be heard - we don't have those this side of the Atlantic...